Convex Optimization for Binary Classifier Aggregation in Multiclass Problems

Multiclass problems are often decomposed into multiple binary problems that are solved by individual binary classifiers whose results are integrated into a final answer. Various methods, including all-pairs (APs), one-versus-all (OVA), and error correcting output code (ECOC), have been studied, to decompose multiclass problems into binary problems. However, little study has been made to optimally aggregate binary problems to determine a final answer to the multiclass problem. In this paper we present a convex optimization method for an optimal aggregation of binary classifiers to estimate class membership probabilities in multiclass problems. We model the class membership probability as a softmax function which takes a conic combination of discrepancies induced by individual binary classifiers, as an input. With this model, we formulate the regularized maximum likelihood estimation as a convex optimization problem, which is solved by the primal-dual interior point method. Connections of our method to large margin classifiers are presented, showing that the large margin formulation can be considered as a limiting case of our convex formulation. Numerical experiments on synthetic and real-world data sets demonstrate that our method outperforms existing aggregation methods as well as direct methods, in terms of the classification accuracy and the quality of class membership probability estimates.Comment: Appeared in Proceedings of the 2014 SIAM International Conference on Data Mining (SDM 2014

Small Footprint High Flow Rate Microdevice for Rare Target Cell Capture

A novel high flow rate cell capture design was introduced to overcome the limitations of the current technologies or methods for rare target cell capture. Even though the rare target cell capture using BioMEMS technology has great potential for cancer diagnosis, previous rare cell capture research could not overcome the limitations of low flow rate or low recovery rate. Rare cell research requires precise sample preparation for accurate results. A new method of preparation for a single or a precise number of target cell was introduced. Current sample preparation methods which are not suitable for rare cell research, such as CTC capture or single cell analysis do not provide precise cell counts below 100. A cell collection chip was designed and used with a polyimide removed capillary tube to collect an exact number of target cells under a microscope. To optimize the dimensions of the high flow rate design, CFD (Fluent v6.3, ANSYS, Inc., Canonsburg, PA, USA) simulation was used. The design focused on a high flow rate at inlet and low axial and lateral velocities in the cell capture regions with a small footprint. Based on the simulation results, the dimensions for several prototypes were determined and fabricated in PMMA. The CTCs, MCF-7 cells, were captured flow rates up to 750 µL/min from 40% red blood cells with 80% recovery rate using the high flow rate device

Biochemical and genetic characterization of bacteriophage 21 holin: S21 as a membrane protein and beyond

The fate of phage-infected bacteria is determined by the holin, a small membrane protein that triggers disruption of the membrane at a programmed time, allowing a lysozyme to attack the cell wall. S2168, the holin of phage 21, has two transmembrane domains (TMDs) with a predicted N-in, C-in topology. Surprisingly, TMD1 of S2168 was found to be dispensable for function, to behave as a SAR ("signal-anchor-release") domain in exiting the membrane to the periplasm, and to engage in homotypic interactions in the soluble phase. The departure of TMD1 from the bilayer coincides with the lethal triggering of the holin and is accelerated by membrane depolarization. Basic residues added at the N-terminus of S2168 prevent the escape of TMD1 to the periplasm and block hole formation by TMD2. Lysis thus depends on dynamic topology, in that removal of the inhibitory TMD1 from the bilayer frees TMD2 for programmed formation of lethal membrane lesions. Like the holin S of λ, the holin of lambdoid phage 21 (S21) controls lysis by forming holes in the membrane. However, unlike Sλ, these holes are small, serving only to depolarize the membrane facilitating the release and activation of the SAR endolysin, R21. We were able to demonstrate that, unlike Sλ, S2168 forms a “pinhole”, thus macromolecules easily pass through Sλ but not S21 holes. This result again supports our interpretation: when S21 triggers, it only needs to collapse the membrane potential, thus causing release and activation of the membrane-tethered inactive SAR endolysin, but does not form holes in the membrane large enough to allow passage of a pre-folded, active cytoplasmic endolysin. The lysis defective S2168 mutant alleles were isolated throughout the S21 gene. Although the majority of lysis defective mutations occurred in the codons for the TMD2 domain, two mutations were found in the codons for the TMD1. This result suggests that only the TMD2 domain of S2168 is likely to participate in actual hole formation. One can assume that two mutant alleles of TMD1 are involved in two different interactions: (a) TMD1-TMD1 intermolecular interaction, (b) TMD1-TMD2 intramolecular interaction. We showed that there is a specific TMD1-TMD2 interaction. In terms of TMD1-TMD2 interaction, the mutated residues of the two TMD1 mutants might prevent a departure of TMD1 from TMD2, resulting in the lysis defective phenotype. Hopefully, these findings deliver some hints about the mechanism of S2168 hole formation and further provoke more extensive work which is required to provide a definite answer to many questions regarding this matter

Forced Vibration of a Timoshenko Beam Subjected to Stationary and Moving Loads Using the Modal Analysis Method

The modal analysis method (MAM) is very useful for obtaining the dynamic responses of a structure in analytical closed forms. In order to use the MAM, accurate information is needed on the natural frequencies, mode shapes, and orthogonality of the mode shapes a priori. A thorough literature survey reveals that the necessary information reported in the existing literature is sometimes very limited or incomplete, even for simple beam models such as Timoshenko beams. Thus, we present complete information on the natural frequencies, three types of mode shapes, and the orthogonality of the mode shapes for simply supported Timoshenko beams. Based on this information, we use the MAM to derive the forced vibration responses of a simply supported Timoshenko beam subjected to arbitrary initial conditions and to stationary or moving loads (a point transverse force and a point bending moment) in analytical closed form. We then conduct numerical studies to investigate the effects of each type of mode shape on the long-term dynamic responses (vibrations), the short-term dynamic responses (waves), and the deformed shapes of an example Timoshenko beam subjected to stationary or moving point loads

Frequency Domain Spectral Element Model for the Vibration Analysis of a Thin Plate with Arbitrary Boundary Conditions

We propose a new spectral element model for finite rectangular plate elements with arbitrary boundary conditions. The new spectral element model is developed by modifying the boundary splitting method used in our previous study so that the four corner nodes of a finite rectangular plate element become active. Thus, the new spectral element model can be applied to any finite rectangular plate element with arbitrary boundary conditions, while the spectral element model introduced in the our previous study is valid only for finite rectangular plate elements with four fixed corner nodes. The new spectral element model can be used as a generic finite element model because it can be assembled in any plate direction. The accuracy and computational efficiency of the new spectral element model are validated by a comparison with exact solutions, solutions obtained by the standard finite element method, and solutions from the commercial finite element analysis package ANSYS

The Connection between Star-Forming Galaxies, AGN Host Galaxies and Early-Type Galaxies in the SDSS

We present a study of the connection between star-forming galaxies, AGN host galaxies, and normal early-type galaxies in the Sloan Digital Sky Survey (SDSS). Using the SDSS DR5 and DR4plus data, we select our early-type galaxy sample in the color versus color-gradient space, and we classify the spectral types of the selected early-type galaxies into normal, star-forming, Seyfert, and LINER classes, using several spectral line flux ratios. We investigate the slope in the fundamental space for each class of early-type galaxies and find that there are obvious differences in the slopes of the fundamental planes (FPs) among the different classes of early-type galaxies, in the sense that the slopes for Seyferts and star-forming galaxies are flatter than those for normal galaxies and LINERs. This may be the first identification of the systematic variation of the FP slope among the subclasses of early-type galaxies. The difference in the FP slope might be caused by the difference in the degree of nonhomology among different classes or by the difference of gas contents in their merging progenitors. One possible scenario is that the AGN host galaxies and star-forming galaxies are formed by gas-rich merging and that they may evolve into normal early-type galaxies after finishing their star formation or AGN activities.Comment: 5 pages with emulateapj, 2 figures, accepted for publication in the Astrophysical Journal Letter

Embracing Limited and Imperfect Data: A Review on Plant Stress Recognition Using Deep Learning

Plant stress recognition has witnessed significant improvements in recent years with the advent of deep learning. A large-scale and annotated training dataset is required to achieve decent performance; however, collecting it is frequently difficult and expensive. Therefore, deploying current deep learning-based methods in real-world applications may suffer primarily from limited and imperfect data. Embracing them is a promising strategy that has not received sufficient attention. From this perspective, a systematic survey was conducted in this study, with the ultimate objective of monitoring plant growth by implementing deep learning, which frees humans and potentially reduces the resultant losses from plant stress. We believe that our paper has highlighted the importance of embracing this limited and imperfect data and enhanced its relevant understanding

Capella: A Space-only High-frequency Radio VLBI Network Formed by a Constellation of Small Satellites

Very long baseline radio interferometry (VLBI) with ground-based observatories is limited by the size of Earth, the geographic distribution of antennas, and the transparency of the atmosphere. In this whitepaper, we present Capella, a tentative design of a space-only VLBI system. Using four small (<500 kg) satellites on two orthogonal polar low-Earth orbits, and single-band heterodyne receivers operating at frequencies around 690 GHz, the interferometer is able to achieve angular resolutions of approximately 7 microarcsec. Within a total observing time of three days, a near-complete uv plane coverage can be reached, with a 1-sigma point source sensitivity as good as about 6~mJy for an instantaneous bandwidth of 1 GHz. The required downlink data rates of >10 Gbps can be reached through near-infrared laser communication; depending on the actual downlink speed, one or multiple ground communication stations are necessary. We note that all key technologies required for the Capella system are already available, some of them off-the-shelf. Data can be correlated using dedicated versions of existing Fourier transform (FX) software correlators; dedicated routines will be needed to handle the effects of orbital motion, including relativistic corrections. With the specifications assumed in this whitepaper, Capella will be able to address a range of science cases, including: photon rings around supermassive black holes; the acceleration and collimation zones of plasma jets emitted from the vicinity of supermassive black holes; the chemical composition of accretion flows into active galactic nuclei through observations of molecular absorption lines; mapping supermassive binary black holes; the magnetic activity of stars; and nova eruptions of symbiotic binary stars - and, like any substantially new observing technique, has the potential for unexpected discoveries.Comment: 18 pages, 2 figures, 1 table. Whitepaper version 1.0. Living document, will be updated when necessar